Sass and Less support

Symmetry Breaking

非対称性: 極性,軸
Asymmetry: Polality, Axis

Responsive across devices

Migration

移動原理: 走化性,集団運動
Directional migration: Chemotaxis, Collective migration.

Components

Morphogenesis

形態形成: 力学,増殖,配置
Morphogenesis: mechanics, growth, rearrangement

2016年 連携大学院 説明会 が 4月19日(土曜日)に開催されます。 場所は 多細胞システム形成研究センター(神戸 ポートアイランド)です。 詳しくは こちらをご覧ください。

フィジカルバイオロジー研究チームでは研究員を募集しています. JREC-INの案内はこちら

細胞や発生現象に関心のある数理科学の研究者で、研究室の内外の研究者と協力しながら、実験、計測、データ解析、理論の諸アプローチを自由な発想で統合し、生物学の研究課題に取り組める方を求めます。

理化学研究所の基礎科学特別研究員制度日本学術振興会の特別研究員制度による研究員の受入も可能です.

連携大学院制度を利用して大阪大学生命機能研究科から大学院生の受入も行っています. また博士課程後期では理化学研究所の大学院生リサーチ・アソシエイトによる受け入れも可能です. 2016年度募集要項

物理・数理を基盤とする数理科学のアプローチを用い,細胞生物学,発生生物学的課題に取り組んでいます.特に発生初期における,(1)極性・軸形成,(2)細胞の方向性運動・集団運動,(3)上皮シートの形態形成,(4)細胞分化,に取り組んでいます.研究室内外と協力し,実験と理論の相補的なアプローチにより生物データ,数理モデル,理論を統合し,これらの現象の定量的な記述とメカニズムの解明をめざします.

キーワード: 非対称性: 極性,軸. 移動原理: 走化性,集団運動. 形態形成: 力学,増殖,再配置.

With the approaches of mathematical sciences, we are working on cell and developmental biology questions. In particular, among early developmental processes we are interested in (1) polarity and axis formation of cell and body, (2) directional and collective cell migrations, (3) morphogenesis of epithelial sheets, and (4) cell differentiation. Through the collaboration between experiment and theory, we are integrating experimental data, mathematical models and theories to quantitatively describe those processes and understand the mechanisms.

Keywords: Asymmetry: Polarity, Axis. Directional migration: Chemotaxis, Collective migration. Morphogenesis: mechanics, growth, rearrangement.


Laboratory Head
Dr. Tatsuo Shibata 柴田達夫 researchmap researchgate
Research Scientist
Dr. Masayuki Hayakawa 早川 雅之 (JSPS)
Dr. Hitoshi Koyano 小谷野 仁
Dr. Yukiko Nakaya 仲矢 由紀子
Dr. Prabhat Shankar プラバト シャンカ
Dr. Fu-Lai Wen 温 福來
Dr. Takaki Yamamoto 山本 尚貴
Assistant
Ms. Satoko Kinoshita 木下 聖子
Technical Staff
Ms. Yuko Wada 和田 裕子
Ms. Ayako Isomura 磯村 綾子
Ms. Emma Hatanaka 畑中 恵茉 (Osaka Univ.)
Dr. Naotoshi Nakamura 中村 直俊
Dr. Naotoshi Matsushita 松下 勝義
Dr. Katsuhiko Sato 佐藤 勝彦
Dr. Toshinori Namba 難波 利典
Dr. Marcel Hoerning マルセル ホールニング
Dr. Akinori Baba 馬場 昭典
Mr. Satoru Iwatani 岩谷 知
Dr. Tetsuya Hiraiwa 平岩 徹也
Dr. Seirin Lee 李 聖林
Dr. Masatoshi Nishikawa 西川 正俊
Mr. Naohiro Akuzawa 阿久澤 直弘
2017
  • Hiraiwa, Tetsuya , Kuranaga, Erina, Shibata, Tatsuo (2017), Wave propagation of junctional remodeling in collective cell movement of epithelial tissue: Numerical simulation study Frontiers in Cell and Developmental Biology. accepted 10.3389/fcell.2017.00066
  • Wen, Fu-Lai , Wang, Yu-Chiun, Shibata, Tatsuo (2017), Epithelial Folding Driven by Apical or Basal-Lateral Modulation: Geometric Features, Mechanical Inference, and Boundary Effects. Biophysical Journal, 112(12): 2683-2695. doi: 10.1016/j.bpj.2017.05.012
2016
  • Arata, Yukinobu, Hiroshima, Michio, Pack, Chan-Gi, Ramanujam, Ravikrishna, Motegi, Fumio, Nakazato, Kenichi, Shindo, Yuki, Wiseman, Paul W, Sawa, Hitoshi, Kobayashi, Tetsuya J, Brandão, Hugo B, Shibata, Tatsuo and Sako, Yasushi (2016), Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary. Cell Reports, 16(8): 2156–2168. doi: 10.1016/j.celrep.2016.07.047
  • Wen, Fu-Lai , Chen, Hsuan-Yi and Leung, Kwan-tai (2016), Statistics of Actin-Propelled Trajectories in Noisy Environments. Physical Review E, 93(6): 062405. doi: 10.1103/PhysRevE.94.012401
  • Wen, Fu-Lai , Leung, Kwan-tai and Chen, Hsuan-Yi (2016), Spontaneous Symmetry Breaking for Geometrical Trajectories of Actin-Based Motility in Three Dimensions. Physical Review E, 94(1): 012401. doi: 10.1103/PhysRevE.93.062405
2015
  • Sato, Katsuhiko, Tetsuya Hiraiwa, Emi Maekawa, Ayako Isomura, Tatsuo Shibata, and Erina Kuranaga. (2015). Left–Right Asymmetric Cell Intercalation Drives Directional Collective Cell Movement in Epithelial Morphogenesis. Nature Communications 6 10074. doi: 10.1038/ncomms10074
  • Yohei Okubo, Junji Suzuki, Kazunori Kanemaru, Naotoshi Nakamura, Tatsuo Shibata, Masamitsu Iino (2015) Visualization of Ca2+ filling mechanisms upon synaptic inputs in the endoplasmic reticulum of cerebellar Purkinje cells, Journal of Neuroscience 35, 15837-15846 doi: 10.1523/JNEUROSCI.3487-15.2015
  • Naotoshi Nakamura, Tatsuo Shibata, (2015) Bifurcation analysis of a self-organizing signaling system for eukaryotic chemotaxis Japan Journal of Industrial and Applied Mathematics, 32, 807-828 doi: 10.1007/s13160-015-0185-5
  • Katsuhiko Sato, Tetsuya Hiraiwa, Tatsuo Shibata , (2015) Cell chirality induces collective cell migration in epithelial sheet, Physical Review Letters, 115, 188102 doi: 10.1103/PhysRevLett.115.188102
  • Prabhat Shankar, Masatoshi Nishikawa, Tatsuo Shibata, (2015) Adaptive responses limited by Intrinsic Noise. PLoS ONE, 10(8): e0136095. doi: 0.1371/journal.pone.013609
  • Sungrim Seirin Lee, Tatsuo Shibata , (2015) Self-organisation and advective transport in the cell polarity formation for asymmetric cell division, Journall of Theoretical Biology, 382, 1–14 doi: 10.1016/j.jtbi.2015.06.032
2014
  • Tetsuya Hiraiwa, Akihiro Nagamatsu, Naohiro Akuzawa, Masatoshi Nishikawa, Tatsuo Shibata (2014) Relevance of intracellular polarity to accuracy of eukaryotic chemotaxis Physical Biology 11: 5. 056002. doi: 10.1088/1478-3975/11/5/056002
  • Masatoshi Nishikawa, Marcel Hörning, Masahiro Ueda, Tatsuo Shibata (2014) Excitable Signal Transduction Induces Both Spontaneous and Directional Cell Asymmetries in the Phosphatidylinositol Lipid Signaling System for Eukaryotic Chemotaxis Biophysical Journal 106: 723-734. doi: 10.1016/j.bpj.2013.12.023
  • 柴田達夫, 西川正俊, 上田昌宏 (2014) ゆらぎの伴うシグナル伝達系による走化性細胞のロバストな勾配センシング 細胞工学 33: 5. 592-597.
  • 猪股秀彦, 柴田達夫 (2014) サイズの発生学 : 濃度勾配のスケーリング 生物物理 54: 3. 140-145.
2013
  • Tatsuo Shibata, Masatoshi Nishikawa, Satomi Matsuoka, Masahiro Ueda, (2013) Intracellular Encoding of Spatiotemporal Guidance Cues in a Self-Organizing Signaling System for Chemotaxis in Dictyostelium Cells, Biophysical Journal, 105, 2199–209. doi: 10.1016/j.bpj.2013.09.024
  • Inomata, H., Shibata, T., Haraguchi, T. & Sasai, Y., (2013) Scaling of Dorsal-Ventral Patterningby Embryo Size-Dependent Degradation of Spemann’s Organizer Signals , Cell 153, 1296–1311 . doi: 10.1016/j.cell.2013.05.004
  • Tetsuya Hiraiwa, Akinori Baba and Tatsuo Shibata, (2013) Theoretical model for cell migration with gradient sensing and shape deformation , Eur. Phys. J. E (2013) 36: 32. doi: 10.1140/epje/i2013-13032-1
  • Tatsuo Shibata, (2013) STOCHASTIC FLUCTUATIONS AND SPONTANEOUS SYMMETRY BREAKING IN THE CHEMOTAXIS SIGNALING SYSTEM OF DICYOSTELIUM CELLS. In: Engineering of Chemical Complexity: Edited by:Alexander S Mikhailov and Gerhard Ertl. pp. 187-200 World Scientific isbn:978-981-4390-45-3. doi: 10.1142/9789814390460_0009
  • Satomi Matsuoka, Tatsuo Shibata, Masahiro Ueda (2013) Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions , PLoS Computation Biology, 9(1): e1002862. doi: 10.1371/journal.pcbi.1002862
2012
  • Akinori Baba, Tetsuya Hiraiwa, and Tatsuo Shibata, (2012) Directional sensing of deformed cells under faint gradients , Physical Review E, 86, 060901(R), DOI:10.1103/PhysRevE.86.060901
  • Toshinori Namba, Masatoshi Nishikawa,Tatsuo Shibata, (2012) The Relation of Signal Transduction to The Sensitivity and Dynamic Range of Bacterial Chemotaxis , Biophysical Journal, 103: 1390-1399 DOI:10.1016/j.bpj.2012.08.034
  • Tatsuo Shibata, Masatoshi Nishikawa, Satomi Matsuoka, and Masahiro Ueda, (2012) Modeling the self-organized phosphatidylinositol lipid signaling system in chemotactic cells using quantitative image analysis , Journal of Cell Science, 125: 5138-5150. doi:10.1242/jcs.108373.
  • P. Bittihn,M. Hörning, and S. Luther, (2012) Negative curvature boundaries as wave emitting sites for the control of biological excitable media , Physical Review Letters, 109, 118106, 2012 DOI: 10.1103/PhysRevLett.109.118106
  • M. Hörning, (2012) Termination of pinned vortices by high-frequency wave trains in heart-like excitable medium with anisotropic fiber orientation , Physical Review E, 86, 031912, 2012 DOI:10.1103/PhysRevE.86.031912
  • Daiki Endo, Katsuhiko Sato, and Yoshinori Hayakawa. (2012). Oscillatory instability in slow crack propagation in rubber under large deformation . Phys Rev E. 86: 016106. doi:10.1103/PhysRevE.86.016106
  • Hiroshi Ochiai, Naoaki Sakamoto, Kazumasa Fujita, Masatoshi Nishikawa, Ken-Ichi Suzuki, Shinya Matsuura, Tatsuo Miyamoto, Tetsushi Sakuma, Tatsuo Shibata, Takashi Yamamoto (2012) Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos. Proc Natl Acad Sci U S A 109: 27. 10915-10920 doi:10.1073/pnas.1202768109
  • Marcel Hörning, Seiji Takagi, and Kenichi Yoshikawa, (2012) Controlling activation site density by low-energy far-field stimulation in cardiac tissue. Phys. Rev. E 85, 061906, dpi:10.1103/PhysRevE.85.061906
  • Masahiro Takahashi, Tatsuo Shibata, Toshio Yanagida, Yasushi Sako (2012) A protein switch with tunable steepness reconstructed in Escherichia coli cells with eukaryotic signaling proteins. Biochem Biophys Res Commun 421: 4. 731-735 May doi:10.1016/j.bbrc.2012.04.071
2011
  • Hibino K, Shibata T, Yanagida T, Sako Y (2011) Activation Kinetics of RAF Protein in the Ternary Complex of RAF, RAS-GTP, and Kinase on the Plasma Membrane of Living Cells: SINGLE-MOLECULE IMAGING ANALYSIS. J Biol Chem 286:36460–36468. doi:10.1074/jbc.M111.262675
  • Kobayashi Y, Shibata T, Kuramoto Y, Mikhailov AS (2011) Robust network clocks: Design of genetic oscillators as a complex combinatorial optimization problem. Phys Rev E 83:060901. dpi:10.1103/PhysRevE.83.060901
  • Ooyama S, Shibata T (2011) Hierarchical organization of noise generates spontaneous signal in Paramecium cell. J Theor Biol 283:1–9. doi:10.1016/j.jtbi.2011.05.016
  • Tatsuo Shibata (2011) Noisy Signal Transduction in Cellular Systems In: Cell Signaling Reactions Edited by: Yasushi Sako, Masahiro Ueda. 297-324 Springer Netherlands isbn:978-90-481-9863-4 DOI:10.1007/978-90-481-9864-1_13
  • 柴田達夫, 上田昌宏 (2011) 細胞における情報処理の確率性と自発的対称性の破れ In: 生命科学の新しい潮流 理論生物学 Edited by:望月敦史. 97-115 共立出版 isbn:978-4320057135
  • 柴田達夫 (2011) バクテリア走化性のシステム論的実験と理論の展開 In: 生命科学の新しい潮流 理論生物学 Edited by:望月敦史. 20-37 共立出版 isbn:978-4320057135
2010
  • Shibata, Tatsuo. (2010) Noisy signal transduction in cellular systems , In Cell Signaling Reactions: Single-Molecule Kinetic Analysis. (Sako, Y., Ueda, M., Ed.), 297-324 Springer Netherlands isbn:978-90-481-9863-4: doi:10.1007/978-90-481-9864-1_13
  • Nishikawa M, Shibata T (2010) Nonadaptive Fluctuation in an Adaptive Sensory System: Bacterial Chemoreceptor , PLoS ONE 5(6): e11224. doi:10.1371/journal.pone.0011224
  • Yasuaki Kobayashi, Tatsuo Shibata, Yoshiki Kuramoto, and Alexander S. Mikhailov, (2010) Evolutionary design of oscillatory genetic networks , European Physical Journal B, 76, 167–178, DOI:10.1140/epjb/e2010-00200-9
  • Yoshiyuki Arai*, Tatsuo Shibata*, Satomi Matsuoka, Masayuki Sato, Toshio Yanagida and Masahiro Ueda, (2010), Self-organization of the phosphatidylinositol lipids signaling system for random cell migration , Proc. Natl. Acad. Sci. U.S.A. 107: 12399–12404. : doi:10.1073/pnas.0908278107 selected in Virtual Journal of Biological Physics Research July 15, 2010, Volume 20, Issue 2
  • Ochiai H, Fujita K, Suzuki K, Nishikawa M, Shibata T, Sakamoto N. and Yamamoto T, (2010) Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases , Genes to Cells (2010) 15, 875–885 DOI: 10.1111/j.1365-2443.2010.01425.x
Before 2010
  • Publications list

Contact

Tatsuo Shibata (Ph.D.)
Laboratory Head
Laboratory for Physical Biology
RIKEN Quantitative Biology Center / RIKEN Center for Developmental Biology
2-2-3 Minatojima-minamimachi,
Chuo-ku, Kobe 650-0047, Japan

柴田 達夫
フィジカルバイオロジー研究チーム、チームリーダー
多細胞動態連携室、室長 理化学研究所
生命システム研究センター / 多細胞システム形成研究センター
神戸市中央区港島南町 2-2-3
〒 650-0047,
☎ 078-306-3265

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